you have not violated sec 40A(3) as such. the said section is applicable for business and profession carried on by the assessee.
you should have shown such cash received in your accounts and mentioned in the ITR accordingly.
Sec 50C gets attracted if you sold the real estate properties. since the sale consideration shall be the value of the property adopted for stamp duty purpose.
in my opinion, there is no violation of Sec 269SS, sec says, "NO PERSON SHALL TAKE OR ACCEPT FROM ANY OTHER PERSON ANY LOAN OR DEPOSIT OTHERWISE THAN BY AN ACCOUNT PAYEE CHEQUE OR DRAFT"
penalties is generally levied if there is case of concealment of income. Mens rea (guilty mind) is to be proved by the dept. if you have not made any profit in accordance with the provisions of income tax Act then no penalty will be charged. further, according to sec 148, a notice for block assessment shall be issued within 4 years or 6 years(if the income is or likely to exceed Rs. 100000) as the case may be.